[gmx-users] PBC problem in bilayer system

shahab shariati shahab.shariati at gmail.com
Sun Sep 14 15:52:23 CEST 2014

Dear Justin

I did following:

trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9

Based on your reply*, *I translated all system along the z.

I used x and y according to box dimension.

I used 9, instead of z dimension (8.30034), for z.

When I see **.xtc using vmd, problem was not solved.

Should I increase or decrease z value for -trans option?

Please see the following link:


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